Cells were fixed in a PBS (-) solution containing 1 % formaldehyde and 2 mM DSG for 10 min. ChIP was performed as previously described (Kadota et al, 2017) except that, RIPA buffer was used instead of LB3 lysis buffer at permeabilization and sonication steps. Chromatin lysate from 1-5 × 10^7 organoid cells was prepared using the Covaris S220 sonicator. Illumina compatible libraries were prepared from 20 ng of input DNA or the 2-4 ng ChIP DNA after size selection for 50-400 bp DNA fragments by AMPure XP beads, using the KAPA LTP Library Preparation kit and TruSeq DNA UD Indexes.